Sharif Digital Repository

Background: Angiogenesis inhibition research is a cutting edge area in angiogenesis-dependent disease therapy, especially in cancer therapy. Recently, studies on anti-angiogenic peptides have provided promising results in the field of cancer treatment. Methods: A non-redundant dataset of 135 anti-angiogenic peptides (positive instances) and 135 non anti-angiogenic peptides (negative instances) was used in this study. Also, 20% of each class were selected to construct an independent test dataset (see Additional files 1, 2). We proposed an effective machine learning based R package (AntAngioCOOL) to predict anti-angiogenic peptides. We have examined more than 200 different classifiers to build... 

Herein, we report the preparation of novel magnetic graphene oxide (GO) grafted with brush polymer via surface-initiated reversible addition-fragmentation chain transfer (SI-RAFT) polymerization and its application as a nanocarrier for magnetic- and pH-triggered delivery of doxorubicin anticancer drug. The RAFT agent, DDMAT, was firstly attached to the surface of magnetic GO nanosheets. The DDMAT-functionalized magnetic GO nanosheets were then used to polymerize glycidyl methacrylate (GMA) using an SI-RAFT method. Afterwards, the epoxy rings of the PGMA chains were opened with hydrazine (N2H4) moieties. The resulting nanocomposite was used as a drug carrier for doxorubicin (DOX) as an... 

Herein, we report the preparation of novel magnetic graphene oxide (GO) grafted with brush polymer via surface-initiated reversible addition-fragmentation chain transfer (SI-RAFT) polymerization and its application as a nanocarrier for magnetic- and pH-triggered delivery of doxorubicin anticancer drug. The RAFT agent, DDMAT, was firstly attached to the surface of magnetic GO nanosheets. The DDMAT-functionalized magnetic GO nanosheets were then used to polymerize glycidyl methacrylate (GMA) using an SI-RAFT method. Afterwards, the epoxy rings of the PGMA chains were opened with hydrazine (N2H4) moieties. The resulting nanocomposite was used as a drug carrier for doxorubicin (DOX) as an... 

We have investigated the pathways of stability for NHCs derived from azole, di-azole, n-tetrazole, and ab-tetrazole (1a, 2a, 3a, and 4a, respectively), at the M06/6-311++G** level of theory. Optimization and vibrational frequency calculations of ground states (GS) and transition states (TS) are performed to identify Gibbs free energies and nature of stationary points, respectively. Two possible pathways of stability for 1a-4a are compared and contrasted which entail dimerization through hydrogen bonding (HB) and covalent bonding (CB). The CB pathway comprises head to head (HH) and head to tail (HT) dimerizations. Plausible reaction profiles are illustrated for 1a-4a along with the mechanism... 

In this study, an enzymatic pathway has been developed to replicate the Calvin Cycle by creating the individual steps of the carbon cycle in a bioreactor. The technology known as “artificial photosynthesis” converts CO2 emissions into a variety of intermediates that serve as precursors to high-value products. CO2, light, water, and electricity were used as feedstock. An electrochemical reactor was also studied for the regeneration of active NADH operating at constant electrode potential. Initially, a batch electrochemical reactor containing 80 mL of 0.2 mM NAD+ in Tris-buffer (pH 7.40) was used to evaluate the electrode material operating at normal temperature and pressure. The results... 

Background: Skeletal muscle mass, which is regulated by a balance between muscle protein synthesis and degradation, is an important factor for movement to meet everyday needs, especially in pathological conditions and aging. The purpose of the present investigation was to compare the alterations of the gene expression involved in muscle protein synthesis and degradation signaling pathways induced by two exercise training protocols. Methods: Eight weeks old Wistar rats have been assigned to the present experimental study, which was conducted from August 2018 to October 2018 at the animal laboratory of Tehran University. They were randomly divided into two resistance and endurance training... 

In this work, a novel carrier based-on modified graphene oxide was designed for co-delivery of hydrophobic and hydrophilic anticancer drugs (curcumin (Cur) and doxorubicin (DOX) as the model of drugs). The hydroxyl groups at the edges of graphene oxide (GO) sheets were used as the initiation sites for growing poly(epichlorohydrin) (PCH) chains. Then, hyperbranched polyglycerol (HPG) was grafted on the hydroxyl end groups of PCH (PCH-g-HPG). Pendant chlorines in the main chain of GO-PCH-g-HPG were replaced with hydrazine. The modification of GO sheets with oxygen-rich polymers increased water solubility of graphene oxide. Doxorubicin was loaded onto the nanocarrier by covalent bonding with... 

We report the development of a metastasis-on-a-chip platform to model and track hepatocellular carcinoma (HCC)–bone metastasis and to analyze the inhibitory effect of an herb-based compound, thymoquinone (TQ), in hindering the migration of liver cancer cells into the bone compartment. The bioreactor consisted of two chambers, one accommodating encapsulated HepG2 cells and one bone-mimetic niche containing hydroxyapatite (HAp). Above these chambers, a microporous membrane was placed to resemble the vascular barrier, where medium was circulated over the membrane. It was observed that the liver cancer cells proliferated inside the tumor microtissue and disseminated from the HCC chamber to the... 

Histidine rich protein II derived peptide (HRP II 169-182) was investigated by molecular dynamics, MD, simulation and 17O electric field gradient, EFG, tensor calculations. MD simulation was performed in water at 300 K with α-helix initial structure. It was found that peptide loses its initial α-helix structure rapidly and is converted to random coil and bent secondary structures. To understand how peptide structure affects EFG tensors, initial structure and final conformations resulting from MD simulations were used to calculate 17O EFG tensors of backbone carbonyl oxygens. Calculations were performed using B3LYP method and 6-31 + G* basis set. Calculated 17O EFG tensors were used to... 

A Quantitative Structure-Retention Relationship (QSRR) study of 32 benzodiazepines is performed in this work. Two feature selection methods of Adaptive Neuro Fuzzy Inference System (ANFIS) and a stepwise regression approach adopted for the Multiple Linear Regressions (MLR) were used to predict the Liquid Chromatography-Mass Spectrometry (LC-MS) Retention Time (RT) of these compounds on a Xterra MS C-18 stationary phase. ANFIS and MLR methods were used as variable selection tools and a neural network was employed for predicting the RTs. Tbree descriptors of 3D-MoRSE-signal 06/weighted by atomic polarizabilities (Mor06p), Radial Distribution Function-1.0/weighted by atomic van der Waals... 

13C chemical shieldings and 14N and 2H electric field gradient (EFG) tensors of L-alanylglycine (L-alagly) dipeptide were calculated at RHF/6-31++G and B3LYP/6-31++G levels of theory respectively. For these calculations a crystal structure of this dipeptide obtained from X-ray crystallography was used. Atomic coordinates of different clusters containing several L-alagly molecules were used as input files for calculations. These clusters consist of central and surrounding L-alagly molecules, the latter forming short, strong, hydrogen bonds with the central molecule. Since the calculations did not converge for these clusters, the surrounding L-alagly molecules were replaced by glycine... 

A linear and non-linear quantitative structure-activity relationship (QSAR) study is presented for modeling and predicting heparanase inhibitors' activity. A data set that consisted of 92 derivatives of 2,3-dihydro-1,3-dioxo-1H-isoindole-5-carboxylic acid, furanyl-1,3-thiazol-2-yl and benzoxazol-5-yl acetic acids is used in this study. Among a large number of descriptors, four parameters classified as physico-chemical, topological and electronic indices are chosen using stepwise multiple regression technique. The artificial neural networks (ANNs) model shows superiority over the multiple linear regressions (MLR) by accounting 87.9% of the variances of antiviral potency of the heparanase... 

The dissolution of plasma-sprayed hydroxyapatite (PHA) coatings with different characteristics, produced by various spraying conditions, in a Tris-buffered solution at pH 7.4 was experimentally studied through the measurement of the release of calcium ions. The phase composition of the coatings at surface and interface, and the porosity were evaluated. The analytical modeling revealed that the calcium dissolution process was composed of two stages. The first stage was found to be both surface and diffusion controlled. The second stage was an exactly diffusion-controlled dissolution. In the first stage, the rate of dissolution and the solubility of the coatings with minimum contents of... 

In this work we present results of density functional theory (DFT) calculations on dicopper patellamides and their affinity for molecular oxygen and carbonate. Patellamides are cyclic octapeptides that are produced by a cyanobacterium, and may show promise as therapeutics. Thus, carbonate binding to a dicopper patellamide center gives a stable cyclic octapeptide with a twist of almost 90°. The system exists in close-lying open-shell singlet and triplet spin states with two unpaired electrons in orthogonal σ* orbitals on each metal center. Subsequently, we replaced carbonate with dioxygen and found a stable Cu2(μ-O)2 diamond shaped patellamide core. In this structure the original dioxygen... 

Apatite-coated Ag/AgBr/TiO2 was prepared by deposition of Ag as novel metal to generate electron-hole pairs by extending the excitation wavelength to the visible-light region, AgBr, and hydroxy apatite as photosensitive material and adsorption bioceramic, respectively. The energy dispersive X-ray spectrometry clearly showed the presence of Ti, Ag, Ca, and P elements on the surface of catalyst. The bactericidal experiments in dark media indicated that only the novel catalyst shows inhibiting growth of bacteria in this case. A transmission electron microscopy image illustrated that catalyst nanoparticles adhere to the outer membrane of the cell and act as an inhibitor to the nourishment of... 

A film composed of carbon nanoparticles and poly(diallyldimethylammonium chloride) or CNP-PDDAC is formed in a layer-by-layer deposition process at tin-doped indium oxide (ITO) substrates. Excess positive binding sites within this film in aqueous phosphate buffer at pH 9.5 are quantified by adsorption of iron(III)phthalocyanine tetrasulfonate and indigo carmine. Both anionic redox systems bind with Langmuirian characteristics (K ≈ 105 mol-1 dm3) and show electrochemical reactivity throughout the film at different thicknesses. Therefore, the electrical conductivity in CNP-PDDAC films is good and the positive binding sites are approximately 140 pmol cm-2 per layer. Structural instability of... 

Four compounds β-sitosterol, β-sitosterol-3-O-β-D- glucopyranoside, ursolic acid and 4′,5,6-trihydroxy-3′,7- dimethoxyflavone were characterized from the dichloromethane extract of the aerial parts of Satureja khuzistanica (Lamiaceae), a native medicinal plant growing in Iran, on the basis of spectral analysis and comparing with the data in literature. The natural occurrence of these compounds can be conclusive for the chemotaxonomic characterization of the genus Satureja. © 2006 The Author(s)  

The on-fiber standardization technique for solid-coated solid-phase microextraction (SPME) was studied, and a theoretical model is proposed for the isotropic behavior of adsorption and desorption, based on Fick's law of diffusion and the Langmuir model. The isotropy of the adsorption and desorption of analytes onto and from the surface of porous solid SPME fiber was validated with the use of a commercially available fiber, a 50-μm Carbowax/ templated resin for carbamate pesticide analysis in various sample matrixes, and a self-made polypyrrole fiber for diazepam analysis in blood samples. Time constants were comparable for the adsorption and desorption processes. Equilibrium constants and... 

The effects of water vapor on CO2/CH4 separation using commercially available poly(2,6-dimethyl-1,4-phenylene oxide) (PPO) and Cardo-type polyimide hollow fiber membranes were investigated. Pure methane and CO2/CH4 mixture permeation experiments were carried out in the absence and presence of water vapor (60% RH). Pure methane permeance decreased in the presence of water vapor for both membrane types. The decrease was 28% for hydrophilic Cardo-type polyimide and 6% for hydrophobic PPO membranes. The decline in the permeance was also observed for CO2/CH4 mixture separation through both membranes. However, selectivities of the two membranes were affected differently by water vapor. The... 

Stem cell treatment is promising in the various disorders treatment, but its effect is confined by the adverse conditions in the damaged tissues. The utilization of hydrogels has been suggested as a procedure to defeat this issue by developing the engraftment and survival of injected stem cells. Specifically, injectable hydrogels have drawn much attention due to their shape adaptability, ease of use, and the capability to reach body parts that are hard to access. In this study, the thermosensitive injectable hydrogels based on oxidized alginate, gelatin, and carbon nitride quantum dots (CNQDs) have been fabricated for tissue engineering. The mechanical characteristics of the nanocomposite...